Defence Force Chief David Hurley says the Australian Navy's incursions into Indonesian waters, while enforcing Operation Sovereign Borders, have led to a "go slow" in the military relationship between the two countries.

It found Australian Navy and Customs ships had entered Indonesian waters six times in December and January, when the commanders incorrectly calculated the location of the maritime border.

General Hurley says he cannot disclose how far Australian ships went into Indonesian waters, but said the personnel involved were not using the "appropriate information".

Five recommendations of joint review:

Chief of Joint Operations and Deputy Chief Executive Officer (Border Enforcement) ACBPS consider the review and monitoring processes undertaken by Headquarters Joint Task Force 639 and the Australian Maritime Security Operations Centre for any individual lapses in professional conduct that contributed to incursions by Australian vessels into Indonesian waters.

Chief of Navy consider each incursion by RAN vessels into Indonesian waters during Operation Sovereign Borders, with regard to any individual lapses in professional conduct.

Force preparation training for Australian vessels designated to be assigned to Operation Sovereign Borders should be amended to ensure crews are prepared to conduct operations while remaining outside Indonesian waters.

Range of policies, procedures and operational documents be reviewed as a result of the incursions by Australian vessels into Indonesian waters.

Border Force Capability Division review operational training provided to ACBPS Commanding Officers and Enforcement Commanders to ensure a tactical appreciation of UN Convention on the Law of the Sea.

"It's not a matter of them not knowing where they were. It's a matter of them being in the wrong spot," he told the ABC's AM program.

"Neither in the headquarters nor on the ships, were they using the appropriate information to inform them where the territorial water baselines were.

"If that had been done, they would not have gone inside territorial waters."

General Hurley said "mistakes were made" but he is certain it will not happen again.

"We've got a bit more work to do. You'll see in the recommendations that we need to go a bit further down the track to determine exactly why some decisions were made," he said.

"But frankly, from our point of view, we've acknowledged the mistake.

"We've got to take that on the chin, get on with the job we're doing and a job I think that's achieving results."

The report recommends the Chief of Navy consider whether there had been any "individual lapses in professional conduct".

Both General Hurley and Defence Minister David Johnston say they will leave any disciplinary action to service chiefs.

It's not a matter of them not knowing where they were. It's a matter of them being in the wrong spot.

"From a Defence perspective, all of the hard work that has been done over a long period of time - defence to defence, navy to navy, air force to air force, army to army - has stood us in good stead," he said.

"I'm quietly confident that the relationship is strong. It's a trusted relationship.

"The politics of these things come to the surface and are visible."

He said he wanted to "focus on the positive, not the negative".

Bishop insists relationship is flourishing

Foreign Minister Julie Bishop told AM the Government had inherited "some challenges" in the relationship from the previous Labor government, but insisted dealings between the two countries continue to "flourish".

"We remain in constant communication and we have very productive talks and discussions, very candid and very open," she said.

Ms Bishop has rejected claims from her Indonesian counterpart, foreign affairs minister Marty Natalegawa, that the relationship has deteriorated since the Coalition came to power.

"I keep in touch with foreign minister Natalegawa, we had a very long conversation only last week and it was a very fruitful, very productive discussion," she said.

"We remain friends, we talk about a whole range of things in a very candid and open way."

The incursions are the latest challenge in the key relationship, which suffered a blow in November when it was revealed Australian spies had collected data on the phone calls made by Indonesian president Susilo Bambang Yudhoyono, his wife and senior officials in 2009.

Mr Yudhoyono suspended official military and intelligence cooperation with Australia and set conditions for its resumption, including the development of a code of conduct.

Ms Bishop says Australia has prepared a draft code and is waiting for Indonesia to respond.

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